99% of that forum post is complete and utter nonsense, at least for medieval Europe. The remaining 1% is just me giving them the benefit of the doubt. The vast majority of soldiers in medieval armies were soldiers with at least some degree of professionalization. Many who were not full-time professional soldiers were at least part-time soldiers. What would be the point of sending a huge number of peasants into battle armed with only "pitchforks, knives, sticks, and even pickup tree branches and rocks ?" This is your labor force. These are the people who make all the food. What utility is there in getting these people killed for minimum battlefield effectiveness? Even in periods and regions where militia troops were present alongside professionals, the militias were not just masses of random civilians with sticks. They were quite frequently trained, drilled, and relatively well-equipped segments of society. 13th century Flemish militias, for example, aren't the scum and refuse of society. They're the burghers, the townsmen whose service is a matter of public pride and honor to his guild/municipality.

That's of course without getting into the horrible misinterpretations of the "knights" that post makes. Some of the examples he cites, like the Swiss, aren't even aristocratic. Swiss pikemen were well-trained, well drilled professionals. That's the only kind of soldier that can effectively fight and maneuver in a large pike formation (as the Swiss so famously and so successfully did). The truth of medieval combat is that armies were in fact relatively small because they were largely composed of professional fighting men rather than conscripted masses. Again, what is the point of conscripting peasants with no combat training and no equipment? Medieval commanders did not need economics degrees to realize that killing the labor force did not benefit them in any way whatsoever.

Chiming in for Japan - ashigaru were definitely not just random peasants lifted from their farms, given a spear, and marched off to war. In the large body of soldiers under the group of ashigaru you have many different categories, anywhere between recently drafted farmers to permanent soldiers to elite ashigaru (who were eventually recognised and incorporated into the class of bushi), an not to mention fringe groups such as the ji-samurai - those of the upper levels were not so much different to a low/poor samurai, and as the samurai did not revolt it follows that many of these footsoldiers did not. Whilst initially, many ashigaru recruited were from the large populace of farmers, later as wars lasted longer and were larger, this posed two major problems to commanders - potentially losing a large portion of your army to the harvest/planting season as well as to the war effort itself.

Thus, the progression of recruitment made it such that a more systematic process was needed, and we see this happen during the latter half of the 16th century - wealthier landowners had the people to contribute to the military whilst not affecting agricultural efficiency, and so they did. Simultaneously, the recognition that ashigaru were a staple core to armies and essentially a requirement of victory meant that commanders had to introduce new systems and structures to accommodate these different soldiers - like I said, it's not as if the entire portion of ashigaru soldiers under a daimyo's command were all disorganised rabble.

I mean considering the Ashigaru farmers made up over 90% of armies in Japanese warfare, how come we never hear about former soldiers in the Tokugawa era getting their Yari spears and attacking a Samurai lord's castle?

The Ikko-Ikki rebellion that took place over the 16th century consisted largely of peasant farmers, monks, and local samurai who were very much against the ruling daimyo. This rebellion failed as they had no educated nor experienced leader to follow in and give them direction - whilst they caused a lot of trouble to Nobunaga and other daimyo of the time, they were really nothing more than a (large) nuisance.

I'll also quickly throw in the Sword Hunt commissioned by Hideyoshi as well as the demilitarisation of all armies in Japan following Ieyasu's unification, whereby confiscation of almost all weapons possessed by civilians as well as stringent rules placed on possession of arms meant that this risk was reduced to zero during the Edo period. Also, to compound this, Hideyoshi issued the Separation Edict (which was then carried on by Ieyasu), which effectively prevented a professional soldier from becoming a farmer, and a farmer from becoming anything (other than a wealthier farmer). In the edict he gives commands such as:

If there should be living among you any men formerly in military service who have taken up the life of a peasant ... you are hereby authorised to take them under surveillance and expel them ...

If any peasant abandons his fields, either to ... become a tradesmen or labourer for hire, not only should he punished but the entire village should be brought to justice with him ...

No military retainer who has left his master without permission shall be given employment by another...

Those soldiers who did not 'survive' the Sword Hunt were now legally severed from the main stream of professional soldiers, further cementing the divide and preventing such an uprising from occurring. As you can imagine, not having access to any arms meant that a peasant mob of most sizes could easily and swiftly be dealt with. This final obliteration of any divider between a poor/minimal-landowning samurai and an elite, well-trained and well-rewarded ashigaru, instead placing them both under the category of bushi, further discouraged any uprising from the 'lesser' ranked soldiers.

From the forum post:

...he points out that historically knights and samurais, etc made such a small portion of an army-often less than 2% in battles.

From all the sources I have available right now, the number seems to come around 10 to 20% or thereabouts, not as small as 2%. It varied depending on conditions such as the economy as well as necessity for many different armies, however 2% is neither a realistic, supported, nor valid estimate of the proportion of samurai to their ashigaru counterparts.

Indeed recently the historical narrative has been dismissing elite professionals ... and more and more writings are now glorifying the farmer peasants of Japan for winning the Feudal wars of Medieval Japan.

Glorifying not so much as being realistic. Not only is the laughable terminology of "farmer peasants" being put on an entire group of soldiers, the fact (as stated above) is that many of these ashigaru became permanent soldiers, and could not be classified simply as a farmer who fought with his farming tools. These were trained soldiers, professionals who were part of a standing army. This meant they received more benefits from remaining in their occupation as a professional soldier than risking everything to make a point.

I'll also add this - the question "Why can't they beat small armies of elites such as knights?" seems to pit all of the ashigaru against all the samurai, and makes the assumption that somehow all of the ashigaru in an army could be convinced to unite against the core of samurai. Many ashigaru were not only professional footsoldiers in their own right but also retainers/labourers that served the samurai, and (I think I may have repeated this a couple times, if so, sorry!) since there were so many different ranks and classes of these ashigaru, the chances of a revolt from within the professional ranks of soldiers was highly unlikely.

However I feel like I'm detracting from your original question, so to come back in a (albeit disjointed) circle - peasants can start an uprising, however they had little reason to, being a small portion of the larger trained army and already receiving many benefits. They can beat small armies of elite warriors such as samurai, however they lacked an overall direction and organisation that these professional standing armies had, and so ultimately would crumble.

You've asked a very expansive question, so in order to answer it it's necessary to break it down. I should note that I can only speak for medieval western Europe, and because your question is quite general, I will have to be general in my response.

First, what is a peasant? This may seem like a trite question, but it is not. People use the term to imply any number of things. Is a peasant every non-aristocrat, non-clergyman? If so, then the vast majority of medieval European armies were composed of peasants. Is a property-owning artisan a peasant? How about a free farmer holding allodial land? These seem to have been the classes that made up the bulk of medieval fighting men. If you define peasant as the very poorest landless agricultural laborers, very few medieval soldiers were peasants.

Conscription was not a thing in the Middle Ages. The polities or proto-states lacked the ability, the will, or the need to conscript en masse. Armies were small and relied on professional and semi-professional soldiers. They were raised generally by one of three methods: levy, hire, or out of personal obligation. The dominance of the levy system in raising medieval troops has been greatly overstated, especially for the later period. It was unreliable at best, massively unpopular at worst, and tended to be used only in the case of invasion. There were customary rules on how long one could be compelled to serve as a levy, after which they had to be paid or sent home. In any case, to be levied is not the same as to be conscripted; the state was not going to send a recruiting party out to roust you from your bed and send you to the front. Great aristocrats might face some repercussions from the king or other superiors if they failed to show up with their retinues when called, but Joe the Pigfarmer probably won't. In any case, the poorest serfs and beggars simply were not called upon to do much (any) fighting, for the simple reason that they were untrained and unequipped and not worth the expense and bother of bringing along. Medieval armies did not use cannon fodder. The Assizes of Arms of Henry II and Henry III make this clear: any man not wealthy enough to own a bow or a spear and shield was not expected to participate in even defensive war.

Mercenaries and hired men make up the second category. The hiring of individuals remained a constant of medieval war, but from the 12th century we begin to see evidence of the employment of organized companies under their own leaders. These men likely came from non-aristocratic backgrounds, but in order to have the skills and equipment that made them worth their pay, they probably weren't from the poorest classes, either. In any case, they were professional soldiers, and don't seem to have identified with the peasantry overmuch. Indeed, chronicles and accounts are full of reports of mercenaries behaving in beastly fashion towards the common people - though one must take these with a grain of salt, as aristocratic writers despised mercenaries on principle.

The third category refers to household troops and others who went to war out of personal obligation. Most of the information we have on household troops for the high middle ages is about knights; but we do get hints that less prestigious soldiers were employed. But again, these are professional soldiers. Who are they likely to feel most loyal to - the man who pays, feeds, and arms them, or the people who support their lifestyle?

Finally, it's important to note that, for the most part, medieval peasants lacked class consciousness. They did not know, in the way that those of us who have been influenced by Karl Marx know it, that they were an exploited class of workers dominated by an owner class. That is not how medievals thought of the world. The most common idealized conception of society was that of the three estates. Briefly, society was divided into the aristocrats, the clergy, and the common people; those who fought, those who prayed, and those who worked. That these categories were much less distinct in practice doesn't concern us. These were not seen as classes in conflict with each other, but distinct categories that had to work together to maintain society. When peasants revolted, it was generally to achieve certain, concrete objectives, not to effect a wholesale restructuring of society.

It is not exactly medieval, but if we look at the German Peasants War of 1524-25, we can see the difference in practice. As you might have guessed, peasants throughout much of southern Germany revolted against their landlords. Sounds very typically Marxist, no? Thing is, they (for the most part) did not believe themselves to be revolutionaries. Heiko Oberman has persuasively argued that their goal was not to radically reshape society, but to restore it to an idealized past. They felt that their landlords were eroding traditional rights (they were), violating the social agreement (they were), and generally depriving them of their customary way of life in order to extract as much cash from them as possible. The revolution was largely for the purpose of forcing their lords to be better lords, not to get rid of lords entirely.

Sources:

Blickle, Peter. The Revolution of 1525 : the German Peasants' War from a new perspective.

France, John. Mercenaries and Paid Men.

Gillingham, John. Richard I.

Scribner, Robert W and Gerhard Benecke. The German Peasant War of 1525 : new viewpoints.

Strickland, M.J. Anglo-Norman Warfare.

/u/MI13 covers Europe, so I'll discuss Japan. Just in case you might think the situation is much different there.

The Japanese developed a system called the go system, where households would be bundled into groups of five, and (ideally) expected to provide five of their men for military training as Ashigaru. As with their European counterparts, they were well-trained - at least for Japan. They did not get to be horsemen (musha), and their armor was not quite as good (famously being open in the back, for one particular type), but they were equipped, trained, and capable all the same.

And they did revolt. The Shimabara Rebellion being among the most famous though far from the only one. Indeed, rebellions among the Hyakusho (the farmer/hunter/fisher class) posed far more political danger to the ruling Daimyo than wandering bands of Ronin could ever hope to.

If you are interested in Japan specifically, you may be interested in the Transactions of the Asiatic Society of Japan - a truly massive collection of scholarly journals, many of which are in the public domain.

For an easier route to finding bits on Japanese warfare and the role Ashigaru actually played in it, you can try Samurai Armies 1467-1649 by Stephen Turnbull, though I do not recall him mentioning anything about rebellions. That stuff gets discussed more casually in the Transactions.